Coronavirus Structure, Vaccine and Therapy Development

Coronavirus particles that are responsible for current infectious outbreak - enhancement of electron microscope images
Coronavirus particles that are responsible for current infectious outbreak - enhancement of electron microscope images

Jonathan King (Prof. of Molecular Biology, MIT) and Eric Sundberg (Prof. of Biochemistry, Emory University School of Medicine)

Structure and Organization of Coronaviruses:

Many concerned over the Coronavirus outbreak may find it useful to understand more about Coronaviruses than is currently being communicated by media sources. As long-time structural biologists we offer below basic information on coronavirus, that may be of assistance to those who have not studied virology. 

All viruses are parasites which can only reproduce within cells. Thus, they are very different from bacteria and fungi which are self-reproducing, often in soil, water, organic wastes, sewage or within organisms. 

Animal and plant viruses fall into two general classes, those whose genetic material is long DNA molecules, and those whose genetic material is RNA molecules. Among the DNA viruses are Herpes, Adenoviruses, and Wart viruses. Coronaviruses use RNA molecules to encode their genes, as do influenza viruses, HIV, and rhinoviruses (common cold). The CoV-19 family infects mammals and birds. (There is some circumstantial evidence that the current strain was originally a virus of bats, and was transmitted  to humans either through eating bat meat, or other contact).

The Coronavirus particles are organized with long RNA polymers tightly packed into the center of the particle, and surrounded by a protective capsid, which is a lattice of repeated protein molecules referred to as coat or capsid proteins. The Coronavirus core particle is further surrounded by an outer membrane envelope made of lipids (fats) with proteins inserted. These membranes derive from the cells in which the virus was last assembled, but modified to contain proteins specified by the viral genes.

A key set of the proteins in the outer membrane project out from the particle and are known as spike proteins. It is these proteins which are recognized by receptor proteins on the host cells which will be infected. Another set of proteins are known as hemagglutinins. For influenza viruses it is this protein that is attacked by antibodies induced by the flu vaccine (more below).  (The name comes from the observation that when the protein was mixed into blood samples carrying anti-flu antibodies, the proteins and antibodies clumped together and agglutinated).

Coronaviruses infect primarily human lung cells through a receptor which normally binds the protein Angiotensin Converting Enzyme (ACE). Many Americans take blood pressure medicines that are chemicals which act by inhibiting ACE. The virus spike protein mimics features of the ACE protein, and thus ”fools” the cell into binding the virus. This is followed by incorporation of the virus inside the infected lung cells and release of the Viral RNA. These RNA molecules recruit the cellular apparatus to make hundreds of thousands of copies, and also instruct the cells to synthesize hundreds of thousands of capsid and spike proteins. These assemble into new virus particles which bud out of the cell surface membrane. The cells die and release the newly formed viral particles propagating the infection.

Testing for the Virus:

The nucleotide sequence of the viral RNA molecules is not found in human DNA or RNA sequences. The test for the presence of the virus, thus, tests for the presence of the viral RNA sequences in tissue samples. The current technology is called “RT-PCR”. RT stands for Reverse Transcriptase, an enzyme in the kit which copies RNA sequences into DNA sequences. PCR stands for Polymerase Chain Reaction, which reproduces and amplifies the DNA sequences for subsequent breakdown for determining the order of the individual nucleotides strung together in the original RNA polymer.

The existence of these assays is testimony of the value of prior investment of federal National Institutes of Health and National Science Foundation and Dept. of Energy funds into genomics and sequencing technology. The test requires adequate supplies of the two enzymes (one leading supplier is New England Biolabs), specialized instruments for running the reaction at elevated temperatures (a local supplier include Bio-Rad and Thermo-Fisher), and trained personnel. Dozens of colleges and universities provide the training needed, but not the actual employees applying the tests. Ramping up capacity to be able to perform millions of tests requires $billions in immediate investment.

The Immune System and Vaccine Development:

Our blood, lymph and organs are host to the white cells of the immune system, which are continually checking for the presence of foreign elements such as viruses, bacteria, fungi, parasites, tumor cells, and toxins. These white cells are made in the bone marrow along with red blood cells.  If the response to for example a foreign toxin is intense yielding serious inflammation we call that an allergic response. In the normal course of events white cells that recognize the invader – for example in a person already previously exposed will synthesize antibody molecules and secrete them into the bloodstream. These antibodies bind to the outside of the foreign agent. For viruses it is often the spike proteins that are recognized. Some of these antibodies that bind to the viral spike proteins can prevent the viral particles from infecting the cells. Other white cells (macrophages) can engulf these compromised particles and then are cleared from the circulation.

A second class of white cells are known as “killer” cells. Some of these white cells can recognize a cell that is infected by the virus, and kill those cells. The phlegm that you cough up on a respiratory infection is full of debris from infected cells lysed by killer white cells.

One of the best ways to protect against infection is to stimulate the immune system with a vaccine. For example, the polio vaccine consists of inactivated viral particles. These are unable to initiate an infection, but are recognized by the white cells of the immune system. Over a period of weeks, the white cells that recognize the virus reproduce in the body. These white cells synthesize and secrete antibodies that can bind to the virus in the vaccine. If the individual is then exposed to infectious poliovirus, the circulating antibodies are already present and are able to inactivate the infecting particles. This immunity may last for decades, though that differs depending on the antigen.

Developing a vaccine requires growing large amounts of modified virus, often in animals, or in tissue culture at large scale. A modern alternative is to purify not the complete virus, but the isolated spike proteins. This is safer and easier to scale up. On the other hand, the immune system response to the isolated protein is often not as robust as it is to the organized lattice of the intact virion. Either way, enough material is needed to inject reasonable doses into millions of people.

But before doing this one has to know that the vaccine works to stimulate a protective immune response. This requires recruiting human volunteers to be vaccinated, and then be challenged with the infectious virus. All of this takes time and skilled personnel and $$. However, with sufficient investment, success is highly likely in most cases  (Though high investments in developing an HIV vaccine have not yet been successful). Note that vaccination is typically preventive – most vaccines do not provide relief for someone already infected.

Antiviral Therapies for Infected Individuals

Addressing the health hazards of Coronavirus infections would benefit greatly by anti-viral drugs that act to block the replication of the virus within infected cells, though some may block the attachment and internalization process. Such therapies are in use for other RNA viruses and are generally small molecules, taken as a pill, which act by binding to and interfering with the virus proteins that are needed to replicate the viral RNA. Another class of anti-viral drugs, which are effective with HIV, act by interfering with the synthesis and assembly of the coat proteins into the viral capsid. The US pharmaceutical industry already has the capacity to produce millions of doses of small molecules, so the rate limiting step in this case is more likely to be at the laboratory research and development stage.

Needed Public Investments:

The Congressional vote for an $8.3 billion dollars to speed up the response to the Coronavirus is a step in the right direction. CoV19 and other emerging infectious diseases represent global threats to our national security. Just as we have massive and sustained funding for the military – more than $738 billion next year -and other efforts to fight more traditional and visible threats to our national security, these “invisible” killers require a similar budgetary effort. Absent a change in tax law, this will require transferring funds from Cold War images of national security budgets, to the real security needs of our people.

The system already lacked sufficient funds to continue with vaccine development for the SARS virus, after that threat subsided. We need a scientific and biomedical research infrastructure that can respond to the next threats, and of course a healthcare system and healthcare financing that can insure high quality treatment for all.

Some Resources:

Cornonavirus Structure:

Center for Disease Control and Prevention:

American Public Health Association:

Vaccine Development:

Jonathan King and Eric Sundberg have directed biomedical research projects on viruses and viral proteins supported by the National Institutes of Health and National Science Foundation. They are both members of the Public Affairs Committee of the Biophysical Society